Heritability estimates and effect on lifetime reproductive performance of age at puberty in sows

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Introduction: Pubertal attainment is critical to reproductive longevity in heifers. Previously, four heifer pubertal classifications were identified according to attainment of blood plasma progesterone concentrations > 1 ng/ml: 1) Early; 2) Typical; 3) Start-Stop; and 4) Non-Cycling. Early and Typical heifers initiated and maintained cyclicity, Start-Stop started and then stopped cyclicity and Non-Cycling never initiated cyclicity. Start-Stop heifers segregated into Start-Stop-Discontinuous (SSD) or Start-Stop-Start (SSS), with SSD having similar phenotypes to Non-Cycling and SSS to Typical heifers. We hypothesized that these pubertal classifications are heritable, and loci associated with pubertal classifications could be identified by genome wide association studies (GWAS). Methods: Heifers (n = 532; 2017 - 2022) genotyped on the Illumina Bovine SNP50 v2 or GGP Bovine 100K SNP panels were used for variant component estimation and GWAS. Heritability was estimated using a univariate Bayesian animal model. Results: When considering pubertal classifications: Early, Typical, SSS, SSD, and Non-Cycling, pubertal class was moderately heritable (0.38 ± 0.08). However, when heifers who initiated and maintained cyclicity were compared to those that did not cycle (Early+Typical vs. SSD+Non-Cycling) heritability was greater (0.59 ± 0.19). A GWAS did not identify single nucleotide polymorphisms (SNPs) significantly associated with pubertal classifications, indicating puberty is a polygenic trait. A candidate gene approach was used, which fitted SNPs within or nearby a set of 71 candidate genes previously associated with puberty, PCOS, cyclicity, regulation of hormone secretion, signal transduction, and methylation. Eight genes/regions were associated with pubertal classifications, and twenty-two genes/regions were associated with whether puberty was attained during the trial. Additionally, whole genome sequencing (WGS) data on 33 heifers were aligned to the reference genome (ARS-UCD1.2) to identify variants in FSHR, a gene critical to pubertal attainment. Fisher's exact test determined if FSHR SNPs segregated by pubertal classification. Two FSHR SNPs that were not on the bovine SNP panel were selected for additional genotyping and analysis, and one was associated with pubertal classifications and whether they cycled during the trial. Discussion: In summary, these pubertal classifications are moderately to highly heritable and polygenic. Consequently, genomic tools to inform selection/management of replacement heifers would be useful if informed by SNPs associated with cyclicity and early pubertal attainment.

Functional genomics of reproduction in pigs: Are we there yet?

Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.

Optimizing feeding regimen of replacement gilts to improve their reproductive performance and retention rate of their first 2 parities

The effects of age, body weight (BW), and backfat thickness (BF) of replacement gilts at first estrus and first mating on their subsequent reproductive performance and retention of their first 2 parities as sows was evaluated. A total of 3,025 Danish replacement gilts were categorized by farm (allocated to 4 farms), cross combination, age, BW and BF at first estrus and first mating, estrous cycle number at first mating, and flush feeding before first mating. The result shows that all the factors mentioned above were significantly associated with reproductive performance and retention rates of the first 2 parities. Farm 3 had more piglets born alive per litter (BA) (P < 0.05). Farms 3 and 4 had more healthy piglets per litter (HP) (P < 0.05). Farm 4 had the most piglets weaned per litter (PW) (P < 0.05). Landrace × Landrace × Yorkshire (L × L × Y) replacement gilts had the most total piglets born per litter (TB), BA, HP, PW and a higher retention rate of the 2 parities than Landrace × Yorkshire (L × Y) replacement gilts (P < 0.05). In addition, flush feeding before first mating had the most TB, BA, HP, PW, and a higher retention rate of the 2 parities than no flush feeding (P < 0.05). Because the effects of replacement gilts rearing parameters on reproductive performance traits differed, we used 100 replacement gilts as a unit and the total number of weaned piglets from the first 2 parities as a new index. Replacement gilts undergoing their first estrus between 180 and 210 d of age at 115 to 124.9 kg BW and 14 to 15 mm BF had significantly higher reproductive indexes for their first 2 parities per 100 replacement gilts. Replacement gilts that mated between 210 and 230 d of age at 140 to 149.9 kg BW and 15 to 16 mm BF had optimal reproductive indexes. These results provide a new insight into the complex relationships among these reproductive performance traits and may help guide successful management of replacement gilts as a pivotal starting point for future fertility and longevity of rearing herds.

Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations

Fecundity is an important economic trait in sheep that directly affects their economic and productive efficiency. Our study aimed to identify SNP loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. Genomic DNA was obtained from Hetian and Cele Black sheep breeds and used for reduced-representation genome sequencing to identify SNP loci associated with pubertal initiation and litter size. Selective signatures analysis was performed based on the fixation index and nucleotide diversity, followed by pathway analysis of the genes contained in the selected regions. The selected SNP loci in the genes associated with pubertal initiation and litter size were validated using both sheep breeds. In total, 384,718 high quality SNPs were obtained and 376 genes were selected. Functional annotation of genes and enrichment analysis identified 12 genes associated with pubertal initiation and 11 genes associated with litter size. SNP locus validation showed that two SNP on PAK1 and four on ADCY1 may be associated with pubertal initiation, and one SNP on GNAQ gene (NC_040253.1: g.62677376G > A) was associated with litter size in Cele Black sheep. Our results provide new theoretical support for sheep breeding.

Effects of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in gilts

The present study was part of a larger experiment that evaluated litter of origin effects on gilt production. The objectives of this study were to determine the effect of physical or fenceline boar exposure and exogenous gonadotropins on puberty induction and subsequent fertility in a commercial farm environment. The experiment was performed in three replicates. Prepubertal gilts were assigned by pen (13/pen) to receive 15 min of daily Fenceline (FBE, n = 153) or Physical (PBE, n = 154) Boar Exposure (BE) for 3 weeks starting at 184 d of age in a purpose-designed Boar Exposure Area (BEAR). At the start of week 3, prepubertal gilts were randomly assigned to receive PG600 or none (Control). From weeks 4 to 6, estrus was checked using only FBE. During weeks 1 to 3, measures of reproductive status were obtained weekly or until expression of estrus. Upon detection of first estrus, gilts were relocated into stalls and inseminated at second estrus. PBE reduced age (P = 0.001) and days to puberty (P = 0.002), increased the proportion of gilts in estrus (P = 0.04) in week 1 (38.3 vs. 27.5%), and tended (P = 0.08) to improve estrus in week 2 (37.6 vs. 26.1%) compared to FBE, respectively. In week 3, more prepubertal gilts receiving PBE-PG600 exhibited estrus (P = 0.04; 81.8%) compared to PBE-Control (40.3%), FBE-PG600 (56.4%), and FBE-Control (47.8%). Overall, expression of estrus through week 6 tended (P = 0.08) to be greater for PBE than FBE (91.5 vs. 85.0%). PBE increased (P ≤ 0.05) or tended to increase (P > 0.05 and ≤0.10) service and farrowing rates in parities 1 through 4, but within parity, there were no effects (P > 0.10) on pig production or wean to service interval. Analyses also indicated that weeks from start of boar exposure to puberty, litter of origin traits, and follicle measures at puberty were related to the subsequent fertility. The results of this study confirm the advantages of using increased intensity of boar exposure, combined with PG600 treatment, for effective induction of pubertal estrus in a commercial setting.

Potential functional variants in AHR signaling pathways are associated with age at puberty in swine

Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.

Evaluation of on-farm indicators of gilt reproductive performance potential at 21 days of age

Selection of replacements for the sow herd is one of the most important facets in swine production. Although our current methods of selection are effective, there is still a large amount of variation in sow reproductive performance traits such as pigs per sow per year (PSY). Therefore, the objective of this study was to determine if on-farm phenotypic traits at 21 d postnatal (PN) or perinatal environmental factors could predict sow reproductive performance. Data were prospectively collected from 2,146 gilts born on a commercial sow production facility and included birth and weaning weights, vulva length and width at 21 d PN, birth and nursing litter size, days nursed, average daily gain from birth to weaning, and age at first estrus. Of the initial animals, 400 (17%) were selected for the sow herd, 353 remained after removal of animals culled for non-reproductive reasons. Animals were assigned to 1 of 5 reproductive performance categories based on observation of estrus or pigs per sow per year (PSY) across two farrowings: High Fertility (HF; 23%; n = 82; ≥26 PSY), Middle Fertility (MF2; 12%; n = 43; 20–25 PSY), Low Fertility (MF3; 15%; n = 54; <20 PSY), Infertile-Estrus (IFe; 10%; n = 36; estrus, no pregnancy), and Infertile-No Estrus (IFno; 39%; n = 138; no estrus, no pregnancy). Generalized linear model analysis indicated vulva width (P = 0.03) was related to PSY, however, it only explained 1.5% of the total variation in PSY. To determine if preweaning variables were predictive of gilt fertility outcome, animals were grouped as those that became pregnant (n = 179) or not (n = 174). Vulva width tended to be greater in fertile animals versus infertile (P = 0.07). Binomial regression analysis revealed a positive relationship between vulva width and gilt fertility, however, this relationship is not strong enough to make sow herd selection decisions.

Associations among individual gilt birth weight, litter birth weight phenotype, and the efficiency of replacement gilt production

Selection for larger litter size has increased the number of low individual birth weight (BWi) pigs and produced sows with a repeatable low average litter birth weight phenotype (BWP). Using an average of 3.6 litters records per sow, BWP was established in 644 nucleus-multiplication sows producing replacement gilts in a large commercial operation and classified as low (L-BWP, <1.18 kg, n = 85), medium (M-BWP, ≥1.18 to ≤1.35 kg, n = 250), or high (H-BWP, >1.35 kg, n = 309) on the basis of a BWi of 1.18 kg below which there was a high risk of early mortality and the average BWi (1.35 kg) for the population. In subsequent litters, potential replacement gilts born to these sows (n = 7,341) received a unique identification tag that allowed the impact of BWi, BWP, and their interactions on the efficiency of replacement gilt production to be evaluated. Negative effects of BWi on mortality until day 4 after birth were confirmed (P < 0.05) and cumulative losses to weaning, to day 70 of age, and to final pre-selection at 165 d of age were affected (P ≤ 0.05) by the interaction between BWP and BWi. Among the 2,035 gilts for which records for selection efficiency and production to fourth parity were available, a lower BWi decreased the probability of gilts reaching pubertal estrus (P < 0.05) after 21 and 28 d of boar stimulation starting at 180 d of age, with no effect of BWP. Overall, neither BWi, BWP, nor their interaction affected age at puberty. After breeding, only the main effect of BWP affected productivity and retention in the sow herd. In parities 1 and 2, percent stillborn was higher in litters born to gilts from H-BWP compared with L-BWP dams (P < 0.05), and in parity 2, total born and born alive were lower in sows derived from H-BWP compared with other BWPs. There were no differences in retention based on BWP classes until parity 2, after which retention tended (P ≤ 0.09) to be lower in sows derived from H-BWP compared with L-BWP dams. These results provide evidence that sow BWP is an important factor in the overall efficiency of replacement gilt management. This study also confirms that effective gilt selection and pre-breeding management protocols support excellent sow lifetime productivity and mitigate the risk of a high BWP in the litter of origin affecting retention in the breeding herd.

Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging

The biological function of human ovaries declines along with aging. To identify the underlying molecular changes during ovarian aging, pigs were used as model animals. Genome-wide DNA methylation and transcriptome-wide RNA expression analyses were performed via high-throughput sequencing of ovaries from young pigs (180 days, puberty stage of first ovulation) and old pigs (eight years, reproductive exhaustion stage). The results identified 422 different methylation regions between old and young pigs; furthermore, a total of 2,243 mRNAs, 95 microRNAs, 248 long noncoding RNAs (lncRNAs), and 116 circular RNAs (circRNAs) were differentially expressed during both developmental stages. Gene ontology analysis showed that these genes related to different methylation and expression are involved in the ovarian aging cycle. Specifically, these are involved in cell apoptosis, death effector domain binding, embryonic development, reproduction and fertilization process, ovarian cumulus expansion, and the ovulation cycle. Multigroup cooperative control relationships were also assessed, and competing endogenous RNA (ceRNA) networks were constructed in the ovarian aging cycle. These data will help to clarify ovary age-associated potential molecular changes in DNA methylation and transcriptional patterns over time.

Gilt Management for Fertility and Longevity

Simple Summary

Improving sow lifetime productivity, herd stability, and maximizing lifetime performance and longevity in the sow herd, represent significant challenges to the swine industry. Routine implementation of efficient gilt development unit (GDU) programs which deliver high quality, breeding-eligible gilts to the sow farm is still needed. Good gilt management starts at birth, because litter of origin, lactation management and the application of early selection strategies are early indicators of future performance and efficiency. A failure to select gilts with the greatest reproductive potential and inappropriate management of their physiological state and metabolic condition at service, are key risk factors for poor sow lifetime productivity (SLP). Management practices that deliver gilts with the greatest potential SLP are crucial to the productivity of conventional production systems.

Abstract

Substantial evidence supports successful management of gilts as an absolutely necessary component of breeding herd management and the pivotal starting point for the future fertility and longevity of the breeding herd. Therefore, gilt management practices from birth have the potential to influence the future reproductive performance of the sow herd. A good gilt management program will address several key components such as birth traits that determine the efficiency of replacement gilt production; effective selection of the most fertile gilts for entry to the breeding herd; effective management programs that provide a consistent supply of service eligible gilts; and appropriate management of weight, physiological maturity, and a positive metabolic state at breeding. Good gilt management can largely resolve the existing gap between excellent genetic potential and the more modest sow lifetime productivity typically achieved in the industry. Investment in good gilt development programs from birth represents a foundational opportunity for improving the efficiency of the pork production industry.